The Mycobacterium tuberculosis Pup-proteasome system regulates nitrate metabolism through an essential protein quality control system

Abstract

The human pathogen Mycobacterium tuberculosis (M. tuberculosis) encodes a proteasome that carries out regulated degradation of bacterial proteins. It has been proposed that the proteasome contributes to nitrogen metabolism in M. tuberculosis, although this hypothesis had not been tested. Upon assessing M. tuberculosis growth in several nitrogen sources, we found that a mutant strain lacking the Mycobacterium proteasomal activator Mpa was unable to use nitrate as a sole nitrogen source due to a specific failure in the pathway of nitrate reduction to ammonium. We found that the robust activity by the nitrite reductase complex NirBD depended on expression of the groEL/groES chaperonin genes, which are regulated by the repressor HrcA. We identified HrcA as a likely proteasome substrate, and propose that the degradation of HrcA is required for the full expression of chaperonin genes. Furthermore, our data suggest that degradation of HrcA, along with numerous other proteasome substrates, is enhanced during growth in nitrate to facilitate the de-repression of the chaperonin genes. Importantly, growth in nitrate is the first example of a specific condition that reduces the steady-state levels of numerous proteasome substrates in M. tuberculosis.\n\nSIGNIFICANCE STATEMENTThe proteasome is required for the full virulence of M. tuberculosis. However, the extent of its role as a regulator of bacterial physiology remains unclear. In this work, we demonstrate a novel function of the proteasome system in maintaining the expression of essential chaperonin genes. This activity by the proteasome is required for M. tuberculosis to use nitrate as a nitrogen source. Furthermore, we identified a specific growth condition that robustly decreases the abundance of pupylated proteins. This observation strongly suggests the presence of a yet-to-be-determined mechanism of control over the Pup-proteasome system in M. tuberculosis that is induced in nitrate.